auto_annot_Martin2019_with_Smillie2019_Type¶
In [1]:
import besca as bc
import pkg_resources
./conda/envs/besca_test/lib/python3.6/site-packages/scanpy/api/__init__.py:6: FutureWarning: In a future version of Scanpy, `scanpy.api` will be removed. Simply use `import scanpy as sc` and `import scanpy.external as sce` instead. FutureWarning,
Specify folders where .h5ad files are found and their names.¶
The datasets that are already annotated and should be used for training. If you only use one dataset please use list of one.
In [2]:
# the path to the datasets
train_dataset_paths = [pkg_resources.resource_filename('besca', 'datasets/data')]
#the names of the h5ad files
train_datasets = ['Smillie2019_processed.h5ad']
The dataset of interest that should be annotated.
In [3]:
test_dataset = 'Martin2019_processed.h5ad'
test_dataset_path = pkg_resources.resource_filename('besca', 'datasets/data')
Give your analysis a name.
In [4]:
analysis_name = 'auto_annot_Martin2019_with_Smillie2019_Type'
Now specify parameters¶
Specify column name of celltype annotation you want to train on.
In [5]:
celltype ='Type'
Choose a method:
- linear: Support Vector Machine with Linear Kernel
- sgd: Support Vector Machine with Linear Kernel using Stochastic Gradient Descent
- rbf: Support Vector Machine with radial basis function kernel. Very time intensive, use only on small datasets.
- logistic_regression: Standard logistic classifier iwth multinomial loss.
- logistic_regression_ovr: Logistic Regression with one versus rest classification.
- logistic_regression_elastic: Logistic Regression with elastic loss, cross validates among multiple l1 ratios.
In [6]:
method = 'logistic_regression'
Specify merge method if using multiple training datasets. Needs to be either scanorama or naive.
In [7]:
merge = 'scanorama'
Decide if you want to use the raw format or highly variable genes. Raw increases computational time and does not necessarily improve predictions.
In [8]:
use_raw = False
You can choose to only consider a subset of genes from a signature set.
In [9]:
genes_to_use = 'all'
Read in all training and the testing set.¶
In [10]:
adata_trains, adata_pred, adata_orig = bc.tl.auto_annot.read_data(train_paths = train_dataset_paths,train_datasets= train_datasets, test_path= test_dataset_path, test_dataset= test_dataset, use_raw = use_raw)
Transforming to str index.
Reading files
Transforming to str index.
In [11]:
adata_trains[0].obs
Out[11]:
| CELL | Cluster | Health | Location | Subject | celltype_highlevel | nGene | nUMI | original_name | percent_mito | n_counts | n_genes | batch | leiden | dblabel | celltype | cluster_celltype | Type | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | N7.EpiA.AAGCAAGAGTCAAC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 1507 | 7428 | N7.EpiA.AAGCAAGAGTCAAC | 0.057351 | 7428.0 | 1507 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 1 | N7.EpiA.ACGAGGGAGCTGAT-Epi | Enterocyte Progenitors | Non-inflamed | Epi | N7 | Epi | 828 | 2877 | N7.EpiA.ACGAGGGAGCTGAT | 0.009037 | 2877.0 | 828 | N7 | 0 | enterocyte progenitor | epithelial cell | 0: epithelial cell | Epithelial |
| 2 | N7.EpiA.ACGTTTACTGGTAC-Epi | Immature Enterocytes 2 | Non-inflamed | Epi | N7 | Epi | 2318 | 15332 | N7.EpiA.ACGTTTACTGGTAC | 0.133707 | 15332.0 | 2318 | N7 | 7 | immature enterocyte | enterocyte | 7: enterocyte | Epithelial |
| 3 | N7.EpiA.AGAGAATGGTCATG-Epi | Enterocyte Progenitors | Non-inflamed | Epi | N7 | Epi | 884 | 3498 | N7.EpiA.AGAGAATGGTCATG | 0.002001 | 3498.0 | 884 | N7 | 7 | enterocyte progenitor | enterocyte | 7: enterocyte | Epithelial |
| 4 | N7.EpiA.AGAGCGGAGTATGC-Epi | TA 1 | Non-inflamed | Epi | N7 | Epi | 858 | 3261 | N7.EpiA.AGAGCGGAGTATGC | 0.003067 | 3261.0 | 858 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 5 | N7.EpiA.AGATTAACGCCATA-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 2743 | 20160 | N7.EpiA.AGATTAACGCCATA | 0.097123 | 20160.0 | 2743 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 6 | N7.EpiA.AGGATGCTTACAGC-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 812 | 2764 | N7.EpiA.AGGATGCTTACAGC | 0.003618 | 2764.0 | 812 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 7 | N7.EpiA.AGGTACACAGACTC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 3109 | 23926 | N7.EpiA.AGGTACACAGACTC | 0.062192 | 23926.0 | 3109 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 8 | N7.EpiA.AGTCTACTTCTCTA-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1945 | 12338 | N7.EpiA.AGTCTACTTCTCTA | 0.083806 | 12338.0 | 1945 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 9 | N7.EpiA.ATAGTCCTTAACCG-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 2172 | 13869 | N7.EpiA.ATAGTCCTTAACCG | 0.128055 | 13869.0 | 2172 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 10 | N7.EpiA.ATATACGAAGTACC-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1245 | 5765 | N7.EpiA.ATATACGAAGTACC | 0.052559 | 5765.0 | 1245 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 11 | N7.EpiA.ATTCCAACTTTGGG-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1380 | 7240 | N7.EpiA.ATTCCAACTTTGGG | 0.072238 | 7240.0 | 1380 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 12 | N7.EpiA.ATTCGACTGCATAC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 1043 | 3617 | N7.EpiA.ATTCGACTGCATAC | 0.004147 | 3617.0 | 1043 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 13 | N7.EpiA.ATTGAAACCTATGG-Epi | TA 1 | Non-inflamed | Epi | N7 | Epi | 959 | 4008 | N7.EpiA.ATTGAAACCTATGG | 0.003743 | 4008.0 | 959 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 14 | N7.EpiA.CAAGCCCTTGACAC-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1082 | 4640 | N7.EpiA.CAAGCCCTTGACAC | 0.067672 | 4640.0 | 1082 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 15 | N7.EpiA.CACGATGAGCTAAC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 1082 | 3790 | N7.EpiA.CACGATGAGCTAAC | 0.002111 | 3790.0 | 1082 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 16 | N7.EpiA.CAGACATGTTTGTC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 849 | 2844 | N7.EpiA.CAGACATGTTTGTC | 0.001055 | 2844.0 | 849 | N7 | 0 | proliferating transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 17 | N7.EpiA.CAGGAACTCGTTAG-Epi | Secretory TA | Non-inflamed | Epi | N7 | Epi | 1799 | 13535 | N7.EpiA.CAGGAACTCGTTAG | 0.103288 | 13535.0 | 1799 | N7 | 6 | transit amplifying cell | goblet cell | 6: goblet cell | Epithelial |
| 18 | N7.EpiA.CCACGGGAGTTACG-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1097 | 4700 | N7.EpiA.CCACGGGAGTTACG | 0.027234 | 4700.0 | 1097 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 19 | N7.EpiA.CGAGGAGACGAGTT-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1007 | 3832 | N7.EpiA.CGAGGAGACGAGTT | 0.071764 | 3832.0 | 1007 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 20 | N7.EpiA.CGCTAAGATAGCGT-Epi | Immature Goblet | Non-inflamed | Epi | N7 | Epi | 935 | 4147 | N7.EpiA.CGCTAAGATAGCGT | 0.005305 | 4147.0 | 935 | N7 | 6 | immature goblet cell | goblet cell | 6: goblet cell | Epithelial |
| 21 | N7.EpiA.CGGACTCTTGCCTC-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1720 | 9256 | N7.EpiA.CGGACTCTTGCCTC | 0.085566 | 9256.0 | 1720 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 22 | N7.EpiA.CGTCCATGGGTTCA-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 804 | 2824 | N7.EpiA.CGTCCATGGGTTCA | 0.001771 | 2824.0 | 804 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 23 | N7.EpiA.CTGATGGACCCTCA-Epi | Secretory TA | Non-inflamed | Epi | N7 | Epi | 944 | 5081 | N7.EpiA.CTGATGGACCCTCA | 0.031096 | 5081.0 | 944 | N7 | 6 | transit amplifying cell | goblet cell | 6: goblet cell | Epithelial |
| 24 | N7.EpiA.CTTAAGCTTACGAC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 2356 | 15497 | N7.EpiA.CTTAAGCTTACGAC | 0.066271 | 15497.0 | 2356 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 25 | N7.EpiA.GAGCTCCTACCACA-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 1240 | 5349 | N7.EpiA.GAGCTCCTACCACA | 0.005235 | 5349.0 | 1240 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 26 | N7.EpiA.GAGCTCCTGCCTTC-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 3145 | 25630 | N7.EpiA.GAGCTCCTGCCTTC | 0.112563 | 25630.0 | 3145 | N7 | 6 | proliferating transit amplifying cell | goblet cell | 6: goblet cell | Epithelial |
| 27 | N7.EpiA.GATGCAACACGCAT-Epi | TA 2 | Non-inflamed | Epi | N7 | Epi | 981 | 4075 | N7.EpiA.GATGCAACACGCAT | 0.006871 | 4075.0 | 981 | N7 | 0 | transit amplifying cell | epithelial cell | 0: epithelial cell | Epithelial |
| 28 | N7.EpiA.GCGAGAGATCGTTT-Epi | Cycling TA | Non-inflamed | Epi | N7 | Epi | 1422 | 6884 | N7.EpiA.GCGAGAGATCGTTT | 0.107641 | 6884.0 | 1422 | N7 | 8 | proliferating transit amplifying cell | epithelial cell | 8: epithelial cell | Epithelial |
| 29 | N7.EpiA.GGAACTTGTGGCAT-Epi | Enterocytes | Non-inflamed | Epi | N7 | Epi | 924 | 5051 | N7.EpiA.GGAACTTGTGGCAT | 0.072461 | 5051.0 | 924 | N7 | 7 | enterocyte | enterocyte | 7: enterocyte | Epithelial |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 149702 | N110.LPB.TTGAACGGTGCAACGA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1246 | 8584 | N110.LPB.TTGAACGGTGCAACGA | 0.026445 | 8584.0 | 1246 | N110 | 1 | plasma cell | plasma cell | 1: plasma cell | B_cells |
| 149703 | N110.LPB.TTGAACGTCACGCATA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1198 | 7094 | N110.LPB.TTGAACGTCACGCATA | 0.020863 | 7094.0 | 1198 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149704 | N110.LPB.TTGAACGTCCACTGGG-Imm | Plasma | Inflamed | LP | N110 | Imm | 1179 | 7678 | N110.LPB.TTGAACGTCCACTGGG | 0.011071 | 7678.0 | 1179 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149705 | N110.LPB.TTGAACGTCGTACGGC-Imm | CD8+ LP | Inflamed | LP | N110 | Imm | 860 | 2072 | N110.LPB.TTGAACGTCGTACGGC | 0.057432 | 2072.0 | 860 | N110 | 3 | CD8-positive, alpha-beta T cell | T cell or ILC | 3: T cell or ILC | T_cells |
| 149706 | N110.LPB.TTGACTTCATCCTAGA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1420 | 9090 | N110.LPB.TTGACTTCATCCTAGA | 0.016832 | 9090.0 | 1420 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149707 | N110.LPB.TTGACTTTCGTACGGC-Imm | Plasma | Inflamed | LP | N110 | Imm | 1588 | 11496 | N110.LPB.TTGACTTTCGTACGGC | 0.012961 | 11496.0 | 1588 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149708 | N110.LPB.TTGCCGTAGAGCAATT-Imm | CD4+ Activated Fos-lo | Inflamed | LP | N110 | Imm | 814 | 2466 | N110.LPB.TTGCCGTAGAGCAATT | 0.027981 | 2466.0 | 814 | N110 | 3 | activated CD4-positive, alpha-beta T cell | T cell or ILC | 3: T cell or ILC | T_cells |
| 149709 | N110.LPB.TTGCCGTAGTCAAGCG-Imm | Plasma | Inflamed | LP | N110 | Imm | 1223 | 6920 | N110.LPB.TTGCCGTAGTCAAGCG | 0.016763 | 6920.0 | 1223 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149710 | N110.LPB.TTGCCGTGTCAGATAA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1672 | 13511 | N110.LPB.TTGCCGTGTCAGATAA | 0.014063 | 13511.0 | 1672 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149711 | N110.LPB.TTGCCGTGTGTGTGCC-Imm | Plasma | Inflamed | LP | N110 | Imm | 1499 | 11399 | N110.LPB.TTGCCGTGTGTGTGCC | 0.011405 | 11399.0 | 1499 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149712 | N110.LPB.TTGCCGTTCAAAGACA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1036 | 5960 | N110.LPB.TTGCCGTTCAAAGACA | 0.021980 | 5960.0 | 1036 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149713 | N110.LPB.TTGCGTCAGCTCCTTC-Imm | Follicular | Inflamed | LP | N110 | Imm | 853 | 2033 | N110.LPB.TTGCGTCAGCTCCTTC | 0.052632 | 2033.0 | 853 | N110 | 10 | follicular B cell | B cell | 10: B cell | B_cells |
| 149714 | N110.LPB.TTGGAACCATGCCTTC-Imm | Plasma | Inflamed | LP | N110 | Imm | 895 | 5828 | N110.LPB.TTGGAACCATGCCTTC | 0.012011 | 5828.0 | 895 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149715 | N110.LPB.TTGGAACTCTCTGTCG-Imm | Plasma | Inflamed | LP | N110 | Imm | 1313 | 8122 | N110.LPB.TTGGAACTCTCTGTCG | 0.019576 | 8122.0 | 1313 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149716 | N110.LPB.TTGTAGGTCCTTGACC-Imm | Plasma | Inflamed | LP | N110 | Imm | 837 | 4026 | N110.LPB.TTGTAGGTCCTTGACC | 0.034526 | 4026.0 | 837 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149717 | N110.LPB.TTTACTGAGAACAACT-Imm | Plasma | Inflamed | LP | N110 | Imm | 1102 | 7834 | N110.LPB.TTTACTGAGAACAACT | 0.013786 | 7834.0 | 1102 | N110 | 1 | plasma cell | plasma cell | 1: plasma cell | B_cells |
| 149718 | N110.LPB.TTTACTGTCTACGAGT-Imm | Plasma | Inflamed | LP | N110 | Imm | 1432 | 9233 | N110.LPB.TTTACTGTCTACGAGT | 0.014946 | 9233.0 | 1432 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149719 | N110.LPB.TTTATGCAGACGCACA-Imm | Plasma | Inflamed | LP | N110 | Imm | 1343 | 9698 | N110.LPB.TTTATGCAGACGCACA | 0.017014 | 9698.0 | 1343 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149720 | N110.LPB.TTTATGCAGTACTTGC-Imm | Cycling Monocytes | Inflamed | LP | N110 | Imm | 2101 | 6771 | N110.LPB.TTTATGCAGTACTTGC | 0.058189 | 6771.0 | 2101 | N110 | 12 | proliferating monocyte | macrophage | 12: macrophage | Myeloid |
| 149721 | N110.LPB.TTTATGCGTTTACTCT-Imm | Plasma | Inflamed | LP | N110 | Imm | 1166 | 7139 | N110.LPB.TTTATGCGTTTACTCT | 0.021151 | 7139.0 | 1166 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149722 | N110.LPB.TTTATGCTCCGCGTTT-Imm | Macrophages | Inflamed | LP | N110 | Imm | 1545 | 5224 | N110.LPB.TTTATGCTCCGCGTTT | 0.043453 | 5224.0 | 1545 | N110 | 12 | macrophage | macrophage | 12: macrophage | Myeloid |
| 149723 | N110.LPB.TTTATGCTCTTGGGTA-Imm | Plasma | Inflamed | LP | N110 | Imm | 959 | 5389 | N110.LPB.TTTATGCTCTTGGGTA | 0.017257 | 5389.0 | 959 | N110 | 4 | plasma cell | plasma cell | 4: plasma cell | B_cells |
| 149724 | N110.LPB.TTTCCTCAGCGCTCCA-Imm | Plasma | Inflamed | LP | N110 | Imm | 947 | 5470 | N110.LPB.TTTCCTCAGCGCTCCA | 0.024314 | 5470.0 | 947 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149725 | N110.LPB.TTTCCTCAGTACGACG-Imm | Plasma | Inflamed | LP | N110 | Imm | 1164 | 6099 | N110.LPB.TTTCCTCAGTACGACG | 0.020659 | 6099.0 | 1164 | N110 | 4 | plasma cell | plasma cell | 4: plasma cell | B_cells |
| 149726 | N110.LPB.TTTCCTCTCAAAGACA-Imm | Plasma | Inflamed | LP | N110 | Imm | 911 | 4672 | N110.LPB.TTTCCTCTCAAAGACA | 0.034461 | 4672.0 | 911 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149727 | N110.LPB.TTTGCGCAGGGTTCCC-Imm | Macrophages | Inflamed | LP | N110 | Imm | 1172 | 3549 | N110.LPB.TTTGCGCAGGGTTCCC | 0.063398 | 3549.0 | 1172 | N110 | 12 | macrophage | macrophage | 12: macrophage | Myeloid |
| 149728 | N110.LPB.TTTGCGCCATGTCGAT-Imm | Plasma | Inflamed | LP | N110 | Imm | 1356 | 9534 | N110.LPB.TTTGCGCCATGTCGAT | 0.019194 | 9534.0 | 1356 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149729 | N110.LPB.TTTGCGCTCAACGAAA-Imm | CD4+ Activated Fos-hi | Inflamed | LP | N110 | Imm | 858 | 2084 | N110.LPB.TTTGCGCTCAACGAAA | 0.051344 | 2084.0 | 858 | N110 | 3 | activated CD4-positive, alpha-beta T cell | T cell or ILC | 3: T cell or ILC | T_cells |
| 149730 | N110.LPB.TTTGCGCTCAACGGCC-Imm | Plasma | Inflamed | LP | N110 | Imm | 1753 | 12962 | N110.LPB.TTTGCGCTCAACGGCC | 0.019981 | 12962.0 | 1753 | N110 | 2 | plasma cell | plasma cell | 2: plasma cell | B_cells |
| 149731 | N110.LPB.TTTGTCAGTTGACGTT-Imm | Macrophages | Inflamed | LP | N110 | Imm | 965 | 2696 | N110.LPB.TTTGTCAGTTGACGTT | 0.051187 | 2696.0 | 965 | N110 | 12 | macrophage | macrophage | 12: macrophage | Myeloid |
149732 rows × 18 columns
In [12]:
adata_pred.obs
Out[12]:
| CELL | CONDITION | Sample_geo_accession | Sample_title | Subject | tissue | status | 10x chemistry | Sample_relation | Sample_relation_2 | ... | Lane | Subtype | percent_mito | n_counts | n_genes | batch | leiden | dblabel | celltype | cluster_celltype | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| index | |||||||||||||||||||||
| GSM3972009_69.AAACATACACACCA-1 | GSM3972009_69.AAACATACACACCA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Central Memory T cells | 0.012165 | 1233.0 | 500 | pat. 5 | 0 | CD4-positive, alpha-beta memory T cell | T cell | 0: T cell |
| GSM3972009_69.AAACATTGGTGTCA-1 | GSM3972009_69.AAACATTGGTGTCA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | unknown | unknown | 0.012548 | 4142.0 | 1277 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AAACGCACTTAGGC-1 | GSM3972009_69.AAACGCACTTAGGC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Activated fibroblasts | 0.006716 | 5806.0 | 1727 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AAACGCTGCTACCC-1 | GSM3972009_69.AAACGCTGCTACCC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Tregs | 0.010526 | 1327.0 | 627 | pat. 5 | 5 | regulatory T cell | T cell | 5: T cell |
| GSM3972009_69.AAACTTGAGTCACA-1 | GSM3972009_69.AAACTTGAGTCACA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Pericytes | 0.013407 | 3803.0 | 1327 | pat. 5 | 21 | pericyte cell | pericyte cell | 21: pericyte cell |
| GSM3972009_69.AAACTTGATCACCC-1 | GSM3972009_69.AAACTTGATCACCC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgA plasma cells | 0.006319 | 6330.0 | 864 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAAGACGAATCACG-1 | GSM3972009_69.AAAGACGAATCACG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Plasmablasts | 0.015349 | 10294.0 | 2204 | pat. 5 | 19 | proliferating T cell | T cell | 19: T cell |
| GSM3972009_69.AAAGACGAATGCTG-1 | GSM3972009_69.AAAGACGAATGCTG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Resident macrophages | 0.027449 | 1858.0 | 644 | pat. 5 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972009_69.AAAGATCTGTATCG-1 | GSM3972009_69.AAAGATCTGTATCG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | DC2 | 0.017936 | 2732.0 | 870 | pat. 5 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972009_69.AAAGATCTTATCGG-1 | GSM3972009_69.AAAGATCTTATCGG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.004392 | 15480.0 | 920 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAAGCAGAGGTTCA-1 | GSM3972009_69.AAAGCAGAGGTTCA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | DC1 | 0.016954 | 3657.0 | 875 | pat. 5 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972009_69.AAAGCAGATTGGCA-1 | GSM3972009_69.AAAGCAGATTGGCA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Plasmablasts | 0.019023 | 5467.0 | 1233 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAAGCAGATTTCGT-1 | GSM3972009_69.AAAGCAGATTTCGT-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | ACKR1+ endothelial cells | 0.015983 | 1438.0 | 692 | pat. 5 | 14 | blood vessel endothelial cell | endothelial cell | 14: endothelial cell |
| GSM3972009_69.AAAGCCTGACTGTG-1 | GSM3972009_69.AAAGCCTGACTGTG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Activated fibroblasts | 0.087591 | 1643.0 | 816 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AAAGCCTGAGCCTA-1 | GSM3972009_69.AAAGCCTGAGCCTA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Central Memory T cells | 0.017105 | 1520.0 | 595 | pat. 5 | 3 | naive T cell | T cell | 3: T cell |
| GSM3972009_69.AAAGTTTGTCTAGG-1 | GSM3972009_69.AAAGTTTGTCTAGG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Activated fibroblasts | 0.013503 | 7848.0 | 1974 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AAATCAACTTCTTG-1 | GSM3972009_69.AAATCAACTTCTTG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.004730 | 6342.0 | 847 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAATCATGAATGCC-1 | GSM3972009_69.AAATCATGAATGCC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.002807 | 16389.0 | 1288 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAATCCCTGTCGTA-1 | GSM3972009_69.AAATCCCTGTCGTA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.006611 | 8923.0 | 930 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AAATCTGAGCTAAC-1 | GSM3972009_69.AAATCTGAGCTAAC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.015385 | 12282.0 | 1639 | pat. 5 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972009_69.AAATGGGAGGACAG-1 | GSM3972009_69.AAATGGGAGGACAG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgA plasma cells | 0.007100 | 7746.0 | 971 | pat. 5 | 10 | IgM or IgA plasma cell | plasma cell | 10: plasma cell |
| GSM3972009_69.AAATGTTGGTGCTA-1 | GSM3972009_69.AAATGTTGGTGCTA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Activated fibroblasts | 0.027858 | 4519.0 | 1331 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AAATTCGACAACCA-1 | GSM3972009_69.AAATTCGACAACCA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.015620 | 3201.0 | 745 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AACAAACTGGTCAT-1 | GSM3972009_69.AACAAACTGGTCAT-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | DC1 | 0.033011 | 1757.0 | 617 | pat. 5 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972009_69.AACACGTGAAGATG-1 | GSM3972009_69.AACACGTGAAGATG-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.002581 | 13167.0 | 880 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AACACGTGTCGCTC-1 | GSM3972009_69.AACACGTGTCGCTC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.005225 | 8230.0 | 710 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AACACTCTAGCAAA-1 | GSM3972009_69.AACACTCTAGCAAA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Activated fibroblasts | 0.013588 | 4340.0 | 1368 | pat. 5 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972009_69.AACAGAGAATTTCC-1 | GSM3972009_69.AACAGAGAATTTCC-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.006489 | 3081.0 | 525 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AACAGCACTCAGGT-1 | GSM3972009_69.AACAGCACTCAGGT-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | IgG plasma cells | 0.004187 | 10508.0 | 887 | pat. 5 | 11 | IgG plasma cell | plasma cell | 11: plasma cell |
| GSM3972009_69.AACAGCACTGCACA-1 | GSM3972009_69.AACAGCACTGCACA-1 | Involved | GSM3972009 | Ileal Involved 69 | pat. 5 | ileal | Involved | V1 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 69.0 | Central Memory T cells | 0.015778 | 1331.0 | 533 | pat. 5 | 5 | regulatory T cell | T cell | 5: T cell |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| GSM3972030_209.TTTATGCCATTTGCCC-1 | GSM3972030_209.TTTATGCCATTTGCCC-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Th17 Trm | 0.025601 | 3164.0 | 946 | pat. 16 | 7 | CD8-positive, alpha-beta memory T cell | T cell | 7: T cell |
| GSM3972030_209.TTTATGCGTGCATCTA-1 | GSM3972030_209.TTTATGCGTGCATCTA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Tregs | 0.020492 | 2928.0 | 901 | pat. 16 | 5 | regulatory T cell | T cell | 5: T cell |
| GSM3972030_209.TTTCCTCAGGGCACTA-1 | GSM3972030_209.TTTCCTCAGGGCACTA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.067949 | 1663.0 | 522 | pat. 16 | 18 | memory T cell | T cell | 18: T cell |
| GSM3972030_209.TTTCCTCAGTGGCACA-1 | GSM3972030_209.TTTCCTCAGTGGCACA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Tregs | 0.074179 | 1766.0 | 625 | pat. 16 | 5 | regulatory T cell | T cell | 5: T cell |
| GSM3972030_209.TTTCCTCCAGCTCGCA-1 | GSM3972030_209.TTTCCTCCAGCTCGCA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Tregs | 0.050861 | 2556.0 | 884 | pat. 16 | 5 | regulatory T cell | T cell | 5: T cell |
| GSM3972030_209.TTTCCTCCATTCACTT-1 | GSM3972030_209.TTTCCTCCATTCACTT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.075423 | 2307.0 | 813 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTCCTCGTAGATTAG-1 | GSM3972030_209.TTTCCTCGTAGATTAG-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Resident macrophages | 0.048736 | 3837.0 | 1408 | pat. 16 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972030_209.TTTCCTCGTCGCGGTT-1 | GSM3972030_209.TTTCCTCGTCGCGGTT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.026460 | 3477.0 | 1004 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTCCTCTCCTTCAAT-1 | GSM3972030_209.TTTCCTCTCCTTCAAT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | IgA plasma cells | 0.013345 | 10116.0 | 1344 | pat. 16 | 4 | IgM or IgA plasma cell | plasma cell | 4: plasma cell |
| GSM3972030_209.TTTCCTCTCGAACTGT-1 | GSM3972030_209.TTTCCTCTCGAACTGT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.077309 | 1397.0 | 545 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTGCGCAGACGCACA-1 | GSM3972030_209.TTTGCGCAGACGCACA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Fibroblasts | 0.025401 | 3301.0 | 1504 | pat. 16 | 12 | fibroblast | fibroblast | 12: fibroblast |
| GSM3972030_209.TTTGCGCAGGTAGCCA-1 | GSM3972030_209.TTTGCGCAGGTAGCCA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Memory B cells | 0.052716 | 8744.0 | 2026 | pat. 16 | 2 | memory B cell | B cell | 2: B cell |
| GSM3972030_209.TTTGCGCCAAGTAATG-1 | GSM3972030_209.TTTGCGCCAAGTAATG-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Memory B cells | 0.052926 | 3760.0 | 920 | pat. 16 | 2 | memory B cell | B cell | 2: B cell |
| GSM3972030_209.TTTGCGCCACGGACAA-1 | GSM3972030_209.TTTGCGCCACGGACAA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.034401 | 1686.0 | 605 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTGCGCGTCAGAATA-1 | GSM3972030_209.TTTGCGCGTCAGAATA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Lymphatics | 0.126883 | 2185.0 | 1064 | pat. 16 | 23 | HEV endothelial cell | endothelial cell | 23: endothelial cell |
| GSM3972030_209.TTTGCGCTCAGTCCCT-1 | GSM3972030_209.TTTGCGCTCAGTCCCT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | IgA plasma cells | 0.020774 | 17618.0 | 1489 | pat. 16 | 13 | IgM or IgA plasma cell | plasma cell | 13: plasma cell |
| GSM3972030_209.TTTGCGCTCCAGTAGT-1 | GSM3972030_209.TTTGCGCTCCAGTAGT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Tregs | 0.043265 | 2034.0 | 708 | pat. 16 | 5 | regulatory T cell | T cell | 5: T cell |
| GSM3972030_209.TTTGGTTCAAAGCGGT-1 | GSM3972030_209.TTTGGTTCAAAGCGGT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.067089 | 2370.0 | 878 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTGGTTCAATGTTGC-1 | GSM3972030_209.TTTGGTTCAATGTTGC-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | DC1 | 0.079333 | 8395.0 | 1970 | pat. 16 | 6 | myeloid leukocyte | myeloid leukocyte | 6: myeloid leukocyte |
| GSM3972030_209.TTTGGTTCATTCCTGC-1 | GSM3972030_209.TTTGGTTCATTCCTGC-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Memory B cells | 0.056118 | 4150.0 | 1165 | pat. 16 | 2 | memory B cell | B cell | 2: B cell |
| GSM3972030_209.TTTGGTTGTGTAATGA-1 | GSM3972030_209.TTTGGTTGTGTAATGA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Th17 Trm | 0.031838 | 5370.0 | 1679 | pat. 16 | 0 | CD4-positive, alpha-beta memory T cell | T cell | 0: T cell |
| GSM3972030_209.TTTGGTTTCAAACGGG-1 | GSM3972030_209.TTTGGTTTCAAACGGG-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | IgA plasma cells | 0.060678 | 7136.0 | 1289 | pat. 16 | 13 | IgM or IgA plasma cell | plasma cell | 13: plasma cell |
| GSM3972030_209.TTTGGTTTCCTGCAGG-1 | GSM3972030_209.TTTGGTTTCCTGCAGG-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Th17 Trm | 0.000573 | 3493.0 | 1213 | pat. 16 | 0 | CD4-positive, alpha-beta memory T cell | T cell | 0: T cell |
| GSM3972030_209.TTTGTCAAGCATCATC-1 | GSM3972030_209.TTTGTCAAGCATCATC-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.121032 | 1512.0 | 533 | pat. 16 | 18 | memory T cell | T cell | 18: T cell |
| GSM3972030_209.TTTGTCAAGGTGATTA-1 | GSM3972030_209.TTTGTCAAGGTGATTA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | IgA plasma cells | 0.024231 | 11802.0 | 1626 | pat. 16 | 13 | IgM or IgA plasma cell | plasma cell | 13: plasma cell |
| GSM3972030_209.TTTGTCAGTCTCCCTA-1 | GSM3972030_209.TTTGTCAGTCTCCCTA-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | IgA plasma cells | 0.048219 | 4998.0 | 795 | pat. 16 | 10 | IgM or IgA plasma cell | plasma cell | 10: plasma cell |
| GSM3972030_209.TTTGTCAGTCTCTTAT-1 | GSM3972030_209.TTTGTCAGTCTCTTAT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.031284 | 1822.0 | 749 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
| GSM3972030_209.TTTGTCAGTGTGGTTT-1 | GSM3972030_209.TTTGTCAGTGTGGTTT-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | ILC3 | 0.100821 | 2190.0 | 740 | pat. 16 | 16 | group 3 innate lymphoid cell | ILC3 | 16: ILC3 |
| GSM3972030_209.TTTGTCATCAGTTAGC-1 | GSM3972030_209.TTTGTCATCAGTTAGC-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | Trm | 0.040230 | 1740.0 | 611 | pat. 16 | 0 | CD4-positive, alpha-beta memory T cell | T cell | 0: T cell |
| GSM3972030_209.TTTGTCATCGTCCAGG-1 | GSM3972030_209.TTTGTCATCGTCCAGG-1 | Involved | GSM3972030 | Ileal Involved 209 | pat. 16 | ileal | Involved | V2 | BioSample: https://www.ncbi.nlm.nih.gov/biosam... | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX... | ... | 209.0 | CD8 Trm | 0.030513 | 2884.0 | 976 | pat. 16 | 1 | CD8-positive, alpha-beta cytotoxic T cell | T cell | 1: T cell |
62202 rows × 27 columns
In [ ]:
This function merges training datasets, removes unwanted genes, and if scanorama is used corrects for datasets.
In [13]:
adata_train, adata_pred = bc.tl.auto_annot.merge_data(adata_trains, adata_pred, genes_to_use = genes_to_use, merge = merge)
merging with scanorama using scanorama rn Found 1054 genes among all datasets [[0. 0.55768303] [0. 0. ]] Processing datasets (0, 1) integrating training set calculating intersection
Train the classifier.¶
The returned scaler is fitted on the training dataset (to zero mean and scaled to unit variance).
In [14]:
classifier, scaler = bc.tl.auto_annot.fit(adata_train, method, celltype)
[Parallel(n_jobs=10)]: Using backend LokyBackend with 10 concurrent workers.
[Parallel(n_jobs=10)]: Done 5 out of 5 | elapsed: 11.9min finished
./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/linear_model/_logistic.py:940: ConvergenceWarning:
lbfgs failed to converge (status=1):
STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.
Increase the number of iterations (max_iter) or scale the data as shown in:
https://scikit-learn.org/stable/modules/preprocessing.html
Please also refer to the documentation for alternative solver options:
https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression
Prediction¶
Use fitted model to predict celltypes in adata_pred. Prediction will be added in a new column called 'auto_annot'. Paths are needed as adata_pred will revert to its original state (all genes, no additional corrections). The threshold should be set to 0 or left out for SVM. For logisitic regression the threshold can be set.
In [15]:
adata_predicted = bc.tl.auto_annot.adata_predict(classifier = classifier, scaler = scaler, adata_pred = adata_pred, adata_orig = adata_orig, threshold = 0.1)
Write out metrics to a report file, create confusion matrices and comparative umap plots
In [16]:
%matplotlib inline
bc.tl.auto_annot.report(adata_predicted, celltype, method, analysis_name, train_datasets, test_dataset, False, merge, use_raw, genes_to_use, clustering = 'leiden')
./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/metrics/_classification.py:1272: UndefinedMetricWarning: Precision and F-score are ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior. ./conda/envs/besca_test/lib/python3.6/site-packages/sklearn/metrics/_classification.py:1272: UndefinedMetricWarning: Recall and F-score are ill-defined and being set to 0.0 in labels with no true samples. Use `zero_division` parameter to control this behavior. ... storing 'auto_annot' as categorical
WARNING: saving figure to file figures/umap.ondata_auto_annot_Martin2019_with_Smillie2019_Type.png
WARNING: saving figure to file figures/umap.auto_annot_Martin2019_with_Smillie2019_Type.png
Confusion matrix, without normalization Normalized confusion matrix
In [17]:
import scanpy as sc
sc.pl.umap(adata_predicted, color=[celltype, 'auto_annot'])
sc.pl.umap(adata_predicted, color=[celltype, 'auto_annot'], legend_loc='on data', legend_fontsize=8)
In [18]:
adata_train
Out[18]:
View of AnnData object with n_obs × n_vars = 149732 × 1054
obs: 'CELL', 'Cluster', 'Health', 'Location', 'Subject', 'celltype_highlevel', 'nGene', 'nUMI', 'original_name', 'percent_mito', 'n_counts', 'n_genes', 'batch', 'leiden', 'dblabel', 'celltype', 'cluster_celltype', 'Type'
var: 'ENSEMBL-0', 'SYMBOL', 'n_cells-0', 'total_counts-0', 'frac_reads-0', 'ENSEMBL-1', 'n_cells-1', 'total_counts-1', 'frac_reads-1'
In [ ]: